Antiviruses only scan accessed/modified files. Unless something or someone is accessing that very specific file on USB drive, nothing will detect it.
If you doubleclick it, it will be scanned. If there is an autorun located on USB drive and is pointing to that EXE (or whatever it is), it will be scanned.
Scanning everything because it's there is waste of resources. Thats why no one does it.
So don't worry about it.

That's what I thought. It only gets scanned when it gets accessed. Whether by user interaction or automatically. ie autoruns etc. If you have a virus on your flash drive and you plug it in, it's not going to infect your computer until you try to do something with it. (That I'm aware of anyways). And as soon as you do try to do something to it (ie move, copy, open, etc) it will be detected and dealt with.